To date, which tool would you recommend for aligning reads to reference genome (Homo sapiens)?

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An Ni Zhang

I would recommend you to do an evaluation of BWA, bowtie2, diamond or usearch and so on against basic blast query. To my experience, different tools have different levels of sensitivity and accuracy when searching against different databases. You may also try a two-step search, like our paper in the follow link. Also, no tool can be rapid without sacrificing the accuracy and sensitivity.

https://www.ncbi.nlm.nih.gov/pubmed/27153579

Article ARGs-OAP: Online analysis pipeline for antibiotic resistance...

Peter Ulz

As far as I can tell BWA is now the most widely used. There is also a discussion on aligners here: https://www.biostars.org/p/125020/.

It probably depends on the read length, the amount of sequencing artifacts, which organism you are working on. We have good experiences with BWA (the MEM variant) on Homo sapiens (Illumina) data but I am sure people are not too unhappy with Bowtie2 either.

Only if you want to specifically look into very complicated regions (segmetnal duplications, repeats, LINE/SINE) this might be a detrimental question, else either one of them will probably work well.

I'm not sure whether I have the right to provide the full text.

But the main idea is to do a pre-filtering search and extract target-like sequences. Then use blast to search against the extracted sequences to maintain good precision and sensitivity.